# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 19:01:29 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: (2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]pent-4-ynamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC#C)NC(=O)/C=C/c2ccccc2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 H6R  H6R  "(2~{S})-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]pent-4-ynamide"  ligand  51  28  .  2022-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H6R
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 H6R  C08  C  C     0   0.593  -11.7777  12.0165  69.7270
 H6R  O17  O  O     0  -0.486  -12.2205  11.9593  68.5857
 H6R  C09  C  C1    0  -0.425  -11.2470  10.8455  70.4545
 H6R  C10  C  C1    0  -0.226  -11.1648   9.6542  69.8543
 H6R  C11  C  CR6   0   0.150  -10.6610   8.4095  70.4254
 H6R  C12  C  CR16  0  -0.305  -10.6197   7.2760  69.6096
 H6R  C13  C  CR16  0  -0.238  -10.1462   6.0653  70.0926
 H6R  C14  C  CR16  0  -0.259   -9.7066   5.9683  71.4049
 H6R  C15  C  CR16  0  -0.231   -9.7451   7.0884  72.2296
 H6R  C16  C  CR16  0  -0.314  -10.2171   8.2964  71.7473
 H6R  C06  C  CSP1  0  -0.554  -13.7119  15.1177  72.9046
 H6R  C04  C  CH2   0  -0.602  -12.1211  15.5505  70.8202
 H6R  C03  C  CH1   0  -0.183  -12.1787  14.4037  69.8031
 H6R  N07  N  NH1   0  -0.662  -11.7517  13.1761  70.4156
 H6R  C02  C  C     0   0.561  -11.2662  14.7540  68.6218
 H6R  O01  O  O     0  -0.468  -10.0622  14.5889  68.6870
 H6R  C27  C  CR5   0   0.569  -12.2574  12.6132  64.1230
 H6R  N26  N  NR15  0  -0.631  -11.4814  11.5307  63.9440
 H6R  C25  C  CH2   0  -0.258  -10.4038  11.3976  64.9018
 H6R  C24  C  CH2   0  -0.470  -10.2775  12.8215  65.4451
 H6R  C23  C  CR15  0  -0.423  -11.6904  13.3878  65.3036
 H6R  C22  C  CH2   0  -0.433  -11.7911  14.8937  65.1297
 H6R  C19  C  CH1   0  -0.219  -11.2423  15.6571  66.3310
 H6R  N18  N  NH1   0  -0.638  -11.9002  15.2941  67.5648
 H6R  C20  C  C1    0   0.194  -11.3081  17.1628  66.1753
 H6R  O21  O  O     0  -0.358  -11.5231  17.7374  65.1420
 H6R  H14  H  H     0   0.273  -10.9259  10.9937  71.4797
 H6R  H1   H  H     0   0.263  -11.4991   9.5855  68.8231
 H6R  H16  H  HCR6  0   0.259  -10.9629   7.3488  68.5843
 H6R  H3   H  HCR6  0   0.260  -10.1218   5.1991  69.4444
 H6R  H17  H  HCR6  0   0.261   -9.3364   5.0259  71.7870
 H6R  H4   H  HCR6  0   0.261   -9.4060   7.0170  73.2548
 H6R  H18  H  HCR6  0   0.256  -10.2390   9.1538  72.4079
 H6R  H13  H  H     0   0.278  -14.3523  14.9397  73.7382
 H6R  H11  H  HCH2  0   0.295  -11.0921  15.6882  71.1641
 H6R  H12  H  HCH2  0   0.305  -12.4125  16.4772  70.3209
 H6R  H10  H  HCH1  0   0.291  -13.2110  14.2975  69.4578
 H6R  H23  H  HNH1  0   0.410  -11.2948  13.2099  71.3139
 H6R  H21  H  HCH2  0   0.234  -10.6612  10.6874  65.6938
 H6R  H22  H  HCH2  0   0.250   -9.4907  11.0472  64.4212
 H6R  H8   H  HCH2  0   0.256   -9.9050  12.8393  66.4671
 H6R  H9   H  HCH2  0   0.244   -9.5829  13.3943  64.8246
 H6R  H20  H  HCR5  0   0.291  -12.2842  13.0807  66.1730
 H6R  H6   H  HCH2  0   0.252  -11.2351  15.2001  64.2403
 H6R  H7   H  HCH2  0   0.250  -12.8339  15.1761  64.9630
 H6R  H19  H  HCH1  0   0.305  -10.1782  15.4277  66.4628
 H6R  H24  H  HNH1  0   0.411  -12.9087  15.3391  67.5774
 H6R  H5   H  H     0   0.209  -11.1284  17.7125  67.1179
 H6R  C05  C  CSP   0   0.297  -12.9936  15.3194  71.9628
 H6R  H25  H  HNR5  0   0.394  -11.7271  10.7996  63.2944
 H6R  O28  O  O     0  -0.486  -13.2464  12.9066  63.4719

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 H6R  N26  C27  single    1.344  0.020  1.344
 H6R  N26  C25  single    1.448  0.020  1.448
 H6R  O28  C27  double    1.220  0.020  1.220
 H6R  C27  C23  single    1.522  0.020  1.522
 H6R  C25  C24  single    1.529  0.020  1.529
 H6R  C24  C23  single    1.529  0.020  1.529
 H6R  O21  C20  double    1.202  0.020  1.202
 H6R  C22  C23  single    1.519  0.020  1.519
 H6R  C22  C19  single    1.526  0.020  1.526
 H6R  C20  C19  single    1.515  0.020  1.515
 H6R  C19  N18  single    1.445  0.020  1.445
 H6R  N18  C02  single    1.346  0.020  1.346
 H6R  O01  C02  double    1.217  0.020  1.217
 H6R  C02  C03  single    1.533  0.020  1.533
 H6R  O17  C08  double    1.226  0.020  1.226
 H6R  C10  C11  single    1.459  0.020  1.459
 H6R  C10  C09  double    1.336  0.020  1.336
 H6R  C08  N07  single    1.349  0.020  1.349
 H6R  C08  C09  single    1.477  0.020  1.477
 H6R  C12  C11  aromatic  1.397  0.020  1.397
 H6R  C12  C13  aromatic  1.387  0.020  1.387
 H6R  C03  N07  single    1.437  0.020  1.437
 H6R  C03  C04  single    1.534  0.020  1.534
 H6R  C11  C16  aromatic  1.399  0.020  1.399
 H6R  C13  C14  aromatic  1.387  0.020  1.387
 H6R  C04  C05  single    1.456  0.020  1.456
 H6R  C16  C15  aromatic  1.384  0.020  1.384
 H6R  C14  C15  aromatic  1.391  0.020  1.391
 H6R  C05  C06  triple    1.202  0.020  1.202
 H6R  C10  H1   single    0.930  0.020  1.086
 H6R  C13  H3   single    0.929  0.020  1.085
 H6R  C15  H4   single    0.929  0.020  1.085
 H6R  C20  H5   single    0.930  0.020  1.086
 H6R  C22  H6   single    0.939  0.020  1.096
 H6R  C22  H7   single    0.939  0.020  1.096
 H6R  C24  H8   single    0.939  0.020  1.096
 H6R  C24  H9   single    0.939  0.020  1.096
 H6R  C03  H10  single    0.939  0.020  1.096
 H6R  C04  H11  single    0.939  0.020  1.096
 H6R  C04  H12  single    0.939  0.020  1.096
 H6R  C06  H13  single    0.913  0.020  1.066
 H6R  C09  H14  single    0.930  0.020  1.086
 H6R  C12  H16  single    0.929  0.020  1.085
 H6R  C14  H17  single    0.929  0.020  1.085
 H6R  C16  H18  single    0.929  0.020  1.085
 H6R  C19  H19  single    0.939  0.020  1.096
 H6R  C23  H20  single    0.939  0.020  1.096
 H6R  C25  H21  single    0.939  0.020  1.096
 H6R  C25  H22  single    0.939  0.020  1.096
 H6R  N07  H23  single    0.868  0.020  1.013
 H6R  N18  H24  single    0.868  0.020  1.013
 H6R  N26  H25  single    0.868  0.020  1.013

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 H6R  N07  C08  C09  115.03  3.000
 H6R  C09  C08  O17  123.47  3.000
 H6R  N07  C08  O17  121.50  3.000
 H6R  H14  C09  C10  121.88  3.000
 H6R  H14  C09  C08  117.63  3.000
 H6R  C10  C09  C08  120.49  3.000
 H6R  H1   C10  C11  115.07  3.000
 H6R  H1   C10  C09  117.64  3.000
 H6R  C11  C10  C09  127.28  3.000
 H6R  C16  C11  C12  118.47  3.000
 H6R  C16  C11  C10  123.25  3.000
 H6R  C12  C11  C10  118.28  3.000
 H6R  H16  C12  C13  119.76  3.000
 H6R  H16  C12  C11  119.25  3.000
 H6R  C13  C12  C11  121.00  3.000
 H6R  H3   C13  C14  120.23  3.000
 H6R  H3   C13  C12  119.86  3.000
 H6R  C14  C13  C12  119.91  3.000
 H6R  H17  C14  C15  120.08  3.000
 H6R  H17  C14  C13  120.21  3.000
 H6R  C15  C14  C13  119.71  3.000
 H6R  H4   C15  C16  119.65  3.000
 H6R  H4   C15  C14  119.98  3.000
 H6R  C16  C15  C14  120.37  3.000
 H6R  H18  C16  C15  119.06  3.000
 H6R  H18  C16  C11  120.40  3.000
 H6R  C15  C16  C11  120.54  3.000
 H6R  H13  C06  C05  180.00  3.000
 H6R  H12  C04  H11  106.73  3.000
 H6R  H12  C04  C03  108.74  3.000
 H6R  H11  C04  C03  109.75  3.000
 H6R  H12  C04  C05  109.48  3.000
 H6R  H11  C04  C05  109.69  3.000
 H6R  C03  C04  C05  112.28  3.000
 H6R  H10  C03  C02  109.91  3.000
 H6R  H10  C03  N07  109.40  3.000
 H6R  C02  C03  N07  110.29  3.000
 H6R  H10  C03  C04  108.51  3.000
 H6R  N07  C03  C04  110.18  3.000
 H6R  C02  C03  C04  108.52  3.000
 H6R  H23  N07  C03  119.06  3.000
 H6R  H23  N07  C08  119.50  3.000
 H6R  C03  N07  C08  120.74  3.000
 H6R  N18  C02  O01  124.24  3.000
 H6R  O01  C02  C03  121.10  3.000
 H6R  N18  C02  C03  114.61  3.000
 H6R  C23  C27  N26  107.35  3.000
 H6R  C23  C27  O28  126.43  3.000
 H6R  N26  C27  O28  126.21  3.000
 H6R  H25  N26  C25  122.74  3.000
 H6R  H25  N26  C27  121.94  3.000
 H6R  C25  N26  C27  114.57  3.000
 H6R  H22  C25  H21  107.91  3.000
 H6R  H22  C25  C24  112.76  3.000
 H6R  H21  C25  C24  111.50  3.000
 H6R  H22  C25  N26  111.19  3.000
 H6R  H21  C25  N26  111.30  3.000
 H6R  C24  C25  N26  102.17  3.000
 H6R  H9   C24  H8   107.88  3.000
 H6R  H9   C24  C23  109.91  3.000
 H6R  H8   C24  C23  113.41  3.000
 H6R  H9   C24  C25  109.79  3.000
 H6R  H8   C24  C25  112.17  3.000
 H6R  C23  C24  C25  103.63  3.000
 H6R  H20  C23  C22  109.42  3.000
 H6R  H20  C23  C24  108.86  3.000
 H6R  C22  C23  C24  116.04  3.000
 H6R  H20  C23  C27  105.71  3.000
 H6R  C22  C23  C27  113.02  3.000
 H6R  C24  C23  C27  103.16  3.000
 H6R  H7   C22  H6   106.79  3.000
 H6R  H7   C22  C19  109.51  3.000
 H6R  H6   C22  C19  108.52  3.000
 H6R  H7   C22  C23  109.68  3.000
 H6R  H6   C22  C23  109.72  3.000
 H6R  C19  C22  C23  112.46  3.000
 H6R  H19  C19  C20  105.21  3.000
 H6R  H19  C19  N18  106.67  3.000
 H6R  C20  C19  N18  108.52  3.000
 H6R  H19  C19  C22  109.82  3.000
 H6R  N18  C19  C22  112.52  3.000
 H6R  C20  C19  C22  113.62  3.000
 H6R  H24  N18  C19  117.03  3.000
 H6R  H24  N18  C02  118.60  3.000
 H6R  C19  N18  C02  123.85  3.000
 H6R  H5   C20  O21  121.62  3.000
 H6R  H5   C20  C19  113.54  3.000
 H6R  O21  C20  C19  124.84  3.000
 H6R  C04  C05  C06  180.00  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 H6R  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 H6R  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 H6R  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 H6R  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 H6R  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 H6R  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 H6R  CONST_07  C23  C27  N26  C25     0.00   0.0  0
 H6R  CONST_08  C13  C12  C11  C10   180.00   0.0  0
 H6R  CONST_09  C15  C16  C11  C10   180.00   0.0  0
 H6R  CONST_10  C25  N26  C27  O28   180.00   0.0  0
 H6R  CONST_11  H3   C13  C12  C11   180.00   0.0  0
 H6R  CONST_12  H4   C15  C16  C11   180.00   0.0  0
 H6R  CONST_13  H18  C16  C11  C12   180.00   0.0  0
 H6R  CONST_14  H17  C14  C13  C12   180.00   0.0  0
 H6R  CONST_15  H4   C15  C14  C13   180.00   0.0  0
 H6R  CONST_16  H16  C12  C13  C14   180.00   0.0  0
 H6R  CONST_17  H18  C16  C15  C14   180.00   0.0  0
 H6R  CONST_18  H3   C13  C14  C15   180.00   0.0  0
 H6R  CONST_19  H16  C12  C11  C16   180.00   0.0  0
 H6R  CONST_20  H17  C14  C15  C16   180.00   0.0  0
 H6R  CONST_21  H25  N26  C27  C23   180.00   0.0  0
 H6R  CONST_22  H25  N26  C27  O28     0.00   0.0  0
 H6R  CONST_23  C03  N07  C08  O17     0.00   0.0  0
 H6R  CONST_24  C03  N07  C08  C09   180.00   0.0  0
 H6R  CONST_25  C19  N18  C02  C03   180.00   0.0  0
 H6R  CONST_26  C19  N18  C02  O01     0.00   0.0  0
 H6R  CONST_27  H23  N07  C08  O17   180.00   0.0  0
 H6R  CONST_28  H23  N07  C08  C09     0.00   0.0  0
 H6R  CONST_29  H24  N18  C02  C03     0.00   0.0  0
 H6R  CONST_30  H24  N18  C02  O01   180.00   0.0  0
 H6R  Var_01    C24  C25  N26  C27   -19.64  30.0  1
 H6R  Var_02    C23  C24  C25  N26    28.75  30.0  1
 H6R  Var_03    H21  C25  N26  C27    99.47  30.0  1
 H6R  Var_04    H22  C25  N26  C27  -140.18  30.0  1
 H6R  Var_05    H8   C24  C25  N26   151.45  30.0  1
 H6R  Var_06    H9   C24  C25  N26   -88.62  30.0  1
 H6R  Var_07    H25  N26  C25  C24   170.11  30.0  1
 H6R  Var_08    H21  C25  C24  C23   -90.23  30.0  1
 H6R  Var_09    H22  C25  C24  C23   148.19  30.0  1
 H6R  Var_10    C12  C11  C10  C09  -177.92  30.0  2
 H6R  Var_11    C16  C11  C10  C09     2.03  30.0  2
 H6R  Var_12    H1   C10  C11  C12     1.61  30.0  3
 H6R  Var_13    H1   C10  C11  C16  -178.44  30.0  3
 H6R  Var_14    C11  C10  C09  C08   179.60   0.0  2
 H6R  Var_15    H14  C09  C10  C11    -0.02   0.0  2
 H6R  Var_16    C10  C09  C08  O17     3.45  30.0  2
 H6R  Var_17    N07  C08  C09  C10  -176.96  30.0  1
 H6R  Var_18    C03  C04  C05  C06    30.79  30.0  1
 H6R  Var_19    H1   C10  C09  C08     0.08   0.0  2
 H6R  Var_20    H14  C09  C08  O17  -176.91  30.0  2
 H6R  Var_21    H11  C04  C05  C06   -91.53  30.0  1
 H6R  Var_22    H12  C04  C05  C06   151.67  30.0  1
 H6R  Var_23    H14  C09  C08  N07     2.68  30.0  2
 H6R  Var_24    H1   C10  C09  H14  -179.54   0.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 H6R  chir_01  C03  C02  N07  C04  negativ
 H6R  chir_02  C23  C27  C24  C22  negativ
 H6R  chir_03  C19  N18  C20  C22  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 H6R  plan-1  C08  0.020
 H6R  plan-1  C09  0.020
 H6R  plan-1  C10  0.020
 H6R  plan-1  C11  0.020
 H6R  plan-1  H14  0.020
 H6R  plan-1  H1   0.020
 H6R  plan-2  C10  0.020
 H6R  plan-2  C11  0.020
 H6R  plan-2  C12  0.020
 H6R  plan-2  C13  0.020
 H6R  plan-2  C14  0.020
 H6R  plan-2  C15  0.020
 H6R  plan-2  C16  0.020
 H6R  plan-2  H16  0.020
 H6R  plan-2  H3   0.020
 H6R  plan-2  H17  0.020
 H6R  plan-2  H4   0.020
 H6R  plan-2  H18  0.020
 H6R  plan-3  C03  0.020
 H6R  plan-3  C02  0.020
 H6R  plan-3  O01  0.020
 H6R  plan-3  C19  0.020
 H6R  plan-3  N18  0.020
 H6R  plan-3  H24  0.020
 H6R  plan-4  C08  0.020
 H6R  plan-4  O17  0.020
 H6R  plan-4  C09  0.020
 H6R  plan-4  C03  0.020
 H6R  plan-4  N07  0.020
 H6R  plan-4  H23  0.020
 H6R  plan-5  C27  0.020
 H6R  plan-5  N26  0.020
 H6R  plan-5  C25  0.020
 H6R  plan-5  C23  0.020
 H6R  plan-5  H25  0.020
 H6R  plan-5  O28  0.020
 H6R  plan-6  C19  0.020
 H6R  plan-6  C20  0.020
 H6R  plan-6  O21  0.020
 H6R  plan-6  H5   0.020

